NP-MRD: Showing NP-Card for 1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium (NP0174424)

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Record Information

Version

2.0

Created at

2022-09-03 11:40:16 UTC

Updated at

2022-09-03 11:40:16 UTC

NP-MRD ID

NP0174424

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium

Description

1341-23-7 Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). 1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium is found in Homo sapiens and Mus musculus. 1341-23-7 Is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
    5.5538    0.2289   -0.9262 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2607   -0.7476   -0.8690 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0829   -1.1240   -0.5458 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8615   -2.5094   -0.5195 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0156   -0.1949   -0.2196 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2101    1.1558   -0.2391 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1513    2.0118    0.0828 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9293    1.4592    0.4138 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7262    0.1304    0.4364 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.5497   -0.4675    0.7814 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4376    0.5716    1.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1490    0.7799   -0.1604 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3660    1.5950    0.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1686    1.8830   -0.8837 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5001   -0.6504   -0.5143 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3605   -1.1627    0.4586 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1275   -1.3054   -0.3101 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2337   -2.6424   -0.0153 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7456   -0.6816    0.1268 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4505   -2.9621    0.2797 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1637    1.5637   -0.4980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3254    3.0767    0.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1120    2.1207    0.6623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4575   -1.0357    1.7506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5156    1.2458   -0.9142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9136    1.1491    1.0443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9766    2.5781    0.5783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9614    1.2838   -0.8779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8658   -0.7635   -1.5331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0830   -0.7545    1.3236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5193   -1.2073   -1.2420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0022   -2.8888    0.5260 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5991   -1.7356    0.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10 17  1  0
 17 18  1  0
 17 15  1  0
 15 16  1  0
 10  9  1  0
  9  8  2  0
  8  7  1  0
  7  6  2  0
  6  5  1  0
  5 19  2  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 15 12  1  0
 19  9  1  0
 14 28  1  0
 13 26  1  0
 13 27  1  0
 12 25  1  6
 10 24  1  1
 17 31  1  6
 18 32  1  0
 15 29  1  6
 16 30  1  0
  8 23  1  0
  7 22  1  0
  6 21  1  0
 19 33  1  0
  4 20  1  0
  2  1  1  0
M  CHG  1   9   1
M  END


  Mrv1652310061714192D          

 18 19  0  0  0  0            999 V2000
   -1.4884    0.9479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528    0.1942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034    1.6153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526    0.7754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665    3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323    0.1080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0032   -0.6457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4817   -1.3131    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.3381    4.0431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376    3.2361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8237   -0.7319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  2  0  0  0  0
 13  3  2  0  0  0  0
 13  4  1  0  0  0  0
 13 11  1  0  0  0  0
 14  5  1  0  0  0  0
 15  8  1  0  0  0  0
 16  9  1  0  0  0  0
 17 10  1  0  0  0  0
 18  7  1  0  0  0  0
 18 11  1  0  0  0  0
M  CHG  1  13   1
M  END
> <DATABASE_ID>
NP0174424

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(C(O)C1O)[N+]1=CC=CC(=C1)C(O)=N

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N2O5/c12-10(17)6-2-1-3-13(4-6)11-9(16)8(15)7(5-14)18-11/h1-4,7-9,11,14-16H,5H2,(H-,12,17)/p+1

> <INCHI_KEY>
JLEBZPBDRKPWTD-UHFFFAOYSA-O

> <FORMULA>
C11H15N2O5

> <MOLECULAR_WEIGHT>
255.249

> <EXACT_MASS>
255.097548011

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.54379534423041

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-carbamoyl-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium

> <ALOGPS_LOGP>
-2.24

> <JCHEM_LOGP>
-6.120781883805078

> <ALOGPS_LOGS>
-2.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.990744651010578

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.390918005504384

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6264200820796249

> <JCHEM_POLAR_SURFACE_AREA>
116.89000000000001

> <JCHEM_REFRACTIVITY>
60.834500000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.29e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-carbamoyl-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-17         0                                  
HETATM    1  C   UNK     0      -2.778   1.769   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.152   0.363   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.873   3.015   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.285   1.447   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.044   6.041   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.620   0.202   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.088   5.565   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.006  -1.205   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.564   4.100   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -0.899  -2.451   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      -0.342   2.854   0.000  0.00  0.00           N+1
HETATM   14  O   UNK     0       4.364   7.547   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.334   8.010   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.377   6.041   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.538  -1.366   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.104   4.100   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1   13                                                       
CONECT    4    6   13                                                       
CONECT    5    7   14                                                       
CONECT    6    2    4   10                                                  
CONECT    7    5    8   18                                                  
CONECT    8    7    9   15                                                  
CONECT    9    8   11   16                                                  
CONECT   10    6   12   17                                                  
CONECT   11    9   13   18                                                  
CONECT   12   10                                                            
CONECT   13    3    4   11                                                  
CONECT   14    5                                                            
CONECT   15    8                                                            
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18    7   11                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₅N₂O₅

Average Mass

255.2490 Da

Monoisotopic Mass

255.09755 Da

IUPAC Name

3-carbamoyl-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium

Traditional Name

3-carbamoyl-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium

CAS Registry Number

Not Available

SMILES

OCC1OC(C(O)C1O)[N+]1=CC=CC(=C1)C(O)=N

InChI Identifier

InChI=1S/C11H14N2O5/c12-10(17)6-2-1-3-13(4-6)11-9(16)8(15)7(5-14)18-11/h1-4,7-9,11,14-16H,5H2,(H-,12,17)/p+1

InChI Key

JLEBZPBDRKPWTD-UHFFFAOYSA-O

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Homo sapiens	LOTUS Database	35616633
Mus musculus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
Pentose monosaccharide
Nicotinamide
Pyridine carboxylic acid or derivatives
Monosaccharide
Pyridine
Pyridinium
Vinylogous amide
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Carboxamide group
Primary carboxylic acid amide
Organoheterocyclic compound
Oxacycle
Azacycle
Carboxylic acid derivative
Hydrocarbon derivative
Primary alcohol
Organic oxide
Organonitrogen compound
Organopnictogen compound
Alcohol
Organic nitrogen compound
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a carbohydrate (NICOTINAMIDE_RIBOSE )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.2	ALOGPS
logP	-6.1	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	11.39	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.89 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	60.83 m³·mol⁻¹	ChemAxon
Polarizability	24.54 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0155929

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

940

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium (NP0174424)

MOL for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

3D MOL for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

3D SDF for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

3D-SDF for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

PDB for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

3D PDB for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

SMILES for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

INCHI for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

Structure for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)

3D Structure for NP0174424 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(c-hydroxycarbonimidoyl)-1λ⁵-pyridin-1-ylium)